1. Field of the Invention
This invention relates to silyloxy aromatic alkylating agents that optionally include a probe capable of associating with biological targets. The alkylating agents are activated for reaction by ionic strength.
2. Background of the Related Art
Currently prescribed chemotherapeutic agents acting at the level of DNA are often effective, but their therapeutic index is quite poor, limited by the lack of target specificity. An international research effort has been underway using a wide range of techniques to develop a gene specific drug--a "magic bullet" that is aimed at a single DNA sequence within a cell.
The technological advances allowing for facile DNA synthesis have produced innumerable protocols which rely on custom oligonucleotides, used as probes to screen for complementary sequences within plasmids, chromosomes and DNA libraries. See, for example, Landegren et al., "DNA Diagnostics-Molecular Techniques and Automation", Science, 242, 229 (1988). The specificity of oligonucleotide hybridization has been utilized for "antisense" methods controlling selective expression of genes both in vivo and in vitro. For example, see Miller et al., "Oligonucleotide Inhibitors of Gene Expression in Living Cells: New Opportunities in Drug Design", Ann. Reports in Med. Chem., 23, 295 (1988). Sequence recognition by the binding of probes most often depends on only the non-covalent forces of hydrogen bonding formed between complementary base pairs. Complexation of this type is quite sufficient for many applications, but covalent cross-linking of duplex structures could simplify many of the current protocols and provide new opportunities for processing DNA in a sequence specific manner. Messenger RNA has become a viable target for inhibiting the expression of a desired gene in vivo. See, for example, Toulme et al., "Antimessenger Oligodeoxyribo-Nucleotides: An Alternative to Antisense RNA for Artificial Regulation of Gene Expression--A Review", Gene, 72, 51-58 (1988); and, Stein et al., "Oligodeoxyribo-Nucleotides as Inhibitors of Gene Expression: A Review", Cancer Research, 48, 2659-2668 (1988). Compounds created for this selective reaction have drawn from the advances in site specific modification of DNA. For example, see Barton, "Metals and DNA: Molecular Left-Handed Complements", Science, 233, 727-734 (1986), and Dervan, "Design of Sequence-Specific DNA-Binding Molecules", Science, 232, 464-471 (1986).
Use of such compounds also depends on the synthesis of metabolically stable oligonucleotides that can traverse cell membranes. For example, see Blake et al., "Hybridization Arrest of Globin Synthesis in Rabbit Reticulocyte Lysates and Cells by Oligodeoxyribonucleoside Methylphosphonates", Biochemistry, 24, 6139-6145 (1985). Also, see Agrawal et al., "Oligodeoxynucleoside phosphoramidates and phosphorothioates as inhibitors of human immunodeficiency virus", Proc. Natl. Acad. Sci. U.S.A., 85, 7079-7083 (1988).
Only recently introduced, the technique of oligonucleotide-directed irreversible DNA modification holds great potential as an in vitro tool for molecular biologists. See, for example, Dervan, "Design of Sequence-Specific DNA-Binding Molecules", Science, 232, 464-471 (1986); and Iverson et al., in "Non-enzymatic Sequence-Specific Cleavage of Single-Stranded DNA to Nucleotide Resolution. DNA Methyl Thiolether Probes", J. Am. Chem. Soc., 109, 1241-1243 (1987). Site specificity is enforced by the hybridization of the oligomer-reactant to its complement sequence prior to reagent action. Target selectivity can then be conferred, in theory, to most reactive compounds by attaching them to oligonucleotides. The required prehybridization step, however, generally limits this technique's applicability to accessible single strand polynucleotide targets or duplex probes when triple helical formation is possible, see Maher III et al., "Inhibition of DNA Binding Proteins by Oligonucleotide-Directed Triple Helix Formation", Science, 245, 725-730 (1989); Science 245, 967-971 (1989); and Science, 249, 73-75 (1990).
Site-directed covalent modification is also constrained by the nature of the reactive group incorporated into the oligomer. Although a large number of reactive appendages are available for related use in vitro, as reported by Iverson et al., J. Am. Chem. Soc., 109 (1987) supra; and by Dervan, Science, 232 (1986) supra, only a limited set of these may apply in a controlled activated manner, either in vitro or for in vivo use.
Sequence recognition between synthetic oligonucleotides and macromolecular DNA represent the keystone of numerous techniques required in molecular biology. For example, see Symons, Nucleic Acid Probes, CRC Press, Inc., Boca Raton, Fla. (1989). The fidelity of this process is typically determined only by the hydrogen bonds formed between complementary bases of double and triple helical DNA. Such associations are sufficient for most applications, but covalent stabilization of a target-probe complex could simplify a variety of protocols including those used to diagnose genetic, malignant and infectious diseases; e.g., see discussions by Landegren et al., "DNA-Diagnostic Molecular Techniques and Automation", Science 242, 229 (1988); and Gamper et al., "Reverse Southern Hybridization" Nucleic Acids Research, 14, 9943 (1986).
A general method for this cross-linking has been demonstrated with the construction of oligonucleotide-directed alkylating agent, reported by Knorre et al., "Complementary-Addressed (Sequence-Specific) Modification of Nucleic Acids", Prog. Nucleic Acids Res. Mol. Biol., 32, 291 (1985); Webb and Matteucci, "Sequence-Specific Crosslinking of Deoxyoligonucleotides via Hybridization-Triggered Alkylation", J. Am. Chem. Soc., 108, 2764 (1986); Dervan, "Design of Sequence-Specific DNA-binding Molecules", Science 232, 464 (1986); and Meyer et al., "Efficient, Specific Crosslinking and Cleavage of DNA by Stable, Synthetic Complementary Oligonucleotides", J. Am. Chem. Soc., 111, 8517 (1989). However, limitations are placed on these reagents because of their inherent reactivity. Only mildly reactive species would allow for target recognition to precede covalent modification. An alternative approach has relied on moieties that remain inert until triggered by a chemical or photochemical signal. For example, see Van Houten et al., "Action Mechanism of ABC Excision Nuclease on a DNA Substrate Containing a Psoralen Crosslink at a Defined Position", Proc. Natl. Acad. Sci. U.S.A., 83, 8077 (1986); Lee et al., "Interaction of Psoralen-Derivatized Oligodeoxyribonucleoside Methylphosphonates with Single-Stranded DNA", Biochemistry, 27, 3197 (1988); Iverson et al., "Nonenzymatic Sequence-Specific Cleavage of Single-Stranded DNA to Nucleotide Resolution. DNA Methyl Thiolether Probes", J. Am. Chem. Soc., 109, 1241 (1987); Chatterjee and Rokita, "Inducible Alkylation of DNA Using an Oligonucleotide-Quinone Conjugate", J. Am. Chem. Soc. 112, 6397 (1990); and also see co-pending patent application U.S. Ser. No. 07/442,947, filed on Nov. 29, 1989 the disclosure of which is incorporated by reference herein.
Organosilane compounds have been used as intermediates in the formation of quinone methides in aprotic solvents. For example, see Ramage et al., "Solid Phase Peptide Synthesis: Fluoride Ion Release of Peptide from the Resin", Tet. Lett., 28, 4105 (1987); Mullen and Barany, "A New Fluoridolyzable Anchoring Linkage for Orthogonal Solid Phase Peptide Synthesis", J. Org. Chem. 53, 5240 (1988); Trahanovsky et al., "Observation of Reactive o-Quinodimethanes by Flow NMR", J. Am. Chem. Soc., 110, 6579 (1988); and Angle and Turnbull, "p-Quinone Methide Initiated Cyclization Reactions", J. Am. Chem. Soc., 111, 1136 (1989).
Yabusaki et al., in PCT Published Application No. WO 85/02628, describe cross-linking agents for binding an oligonucleotide probe to a target DNA or RNA molecule. Three types of cross-linking agents are described, including "bi-functional photoreagents", "mixed chemical and biochemical bifunctional reagents" and "bifunctional chemical cross-linking molecules". The bifunctional photoreagents contain two photochemically reactive sites that bind covalently to the probe and to the target molecules. The mixed chemical and photochemical bifunctional reagent is bound non-photochemically to the probe molecule, followed by photochemical binding to the target molecule. Non-photochemical binding is described as a chemical reaction such as alkylation, condensation or additional. Bi-functional chemical cross-linking molecules are said to be activated either catalytically or by high temperature following hybridization.
Although Yabusaki et al. generally hypothesize the concept of a bifunctional photochemical reagent and a mixed chemical and photochemical reagent, there is no specific description of these molecules. All of the reagents they describe are well known photochemical reagents, these include the psoralen derivatives, including furocoumarins, the benzodipyrone derivatives, and the bis-azide derivatives. None of these molecules, however, work on the basis of ionic activation. These reagents, especially the psoralen derivatives, are toxic, causing severe burning of the organism after exposure to sunlight. Finally, the covalent crosslinks formed by psoralens are not permanent, rather, they are degraded by UV irradiation.
Two recent articles reported the use or psoralen crosslinks of DNA substrates, the first by Van Houten et al., in "Action Mechanism of ABC Excision Nuclease on a DNA Substrate Containing a Psoralen Crosslink at a Defined Position", Proc. Natl Acad. Sci. U.S.A., 83, 8077-8081 (1986), and the second by Lee et al., in "Interaction of Psoralen-Derivatized Oligodeoxyribonucleoside Methyl-Phosphonates with Single-Stranded DNA", Biochemistry, 27, 3197-3203 (1988). Both articles reported covalent cross-linking between the DNA molecule and a complementary oligomer that contains a psoralen derivative. The covalent binding of the psoralen derivative to the DNA molecule was activated by UV irradiation. Accordingly, just like the Yakusaki patent application, the covalent crosslinks formed by psoralens are not permanent, being degraded by UV irradiation.
The techniques of Northern and Southern blotting are two of the most powerful and frequently used procedures in molecular biology, see Wall et al., "Northern and Southern Blots", Methods Enz., 152, 572-573 (1987). Yet the necessary manipulations are time consuming and are not likely to be automated under current technology. Often the polynucleotide (RNA, DNA) under analysis must first be fractionated by size, transferred onto a solid support and then treated through a series of steps to ensure only specific binding of a probe. Detection of the hybridized products usually depends on radiolabelling, heavy metal derivatization or antibody complexation. The methods of blotting have been a staple of basic research, and now also serve in an ever increasing number of commercial kits used to diagnose genetic, malignant, and infectious diseases. See Landegren et al., "DNA Diagnostics-Molecular Techniques and Automation", Science, 242, 229 (1988). Related advances have also allowed these processes to aid in forensic science, see Higuchi et al., "DNA Typing from Single Hairs", Nature, 332, 543-546 (1988); and the Human Genome Project, see Conner et al., "Detection of Sickle Cell .beta.'-Globin Allele by Hybridization with Synthetic Oligonucleotides", Proc. Natl. Acad. Sci. U.S.A., 80, 278-282 (1983).
Psoralens have been used to randomly crosslink duplex DNA during hybridization in order to facilitate Southern Blotting procedures. This new test is referred to as Reverse Southern blotting. For example, see Gamper et al., "Reverse Southern Hybridization", Nucl Acids Res., 14, 9943 (1986). Other biochemical and reduction activated reagents are needed to replace or complement psoralens for sequence detection and to provide an alternate set of conditions for duplex stabilization.
Accordingly, none of the related art describes or suggests using ionic activation with aromatic silyloxy alkylating agents in order to permanently alkylate a biological molecule such as DNA.
Therefore, it is a purpose of the present invention to provide a new class of ionically activated alkylating probes which form a permanent covalent crosslink.
Another purpose of the present invention is to provide an ionically activated alkylating probe which can be used in vivo.
A further goal of the present invention is to provide a new class of ionically activated Reverse Southern blotting reagents for conjugating and permanently crosslinking target oligonucleotides and facilitate blotting procedures, sequence detection and nucleic acid fragmentation.